Objective To explore the effect of different disinfection methods on preventing fat liquefaction of cesarean section in obese women during pregnancy. Methods A total of 90 obese pregnant women scheduled for lower uterine cesarean section in Huizhou Third People's Hospital from September 2020 to July 2021 were divided into group A, B and C by random number table method, with 30 cases in each group.Group A, B and C were routinely intervened, and they were disinfected before and during operation with 2% Chlorhexidine Gluconate, Povidone Iodine and 0.5%Iodophor respectively.The incidences of incision fat liquefaction and incision infection, postoperative rehabilitation and hospitalization expenses were compared among the three groups. Results The incidence of incision fat liquefaction and incision infection in group A were lower than those in group C,with statistically significant differences(P＜0.01),and there was no statistically significant difference in the above indicators of group B compared with group A and group C (P＞0.05).The anal exhaust time, indwelling catheterization time, time to get out of bed for the first time and time to eat for the first time in group A and group B were shorter than those in group C, and the above times in group A were shorter than those in group B, and the hospitalization time in group A was shorter than that in group C, then the hospitalization expenses of group A and group B were less than those in group C, and the hospitalization expenses of group A were less than those in group B, with statistically significant differences (P＜0.05). Conclusion Compared with Povidone Iodine and Iodophor, Chlorhexidine Gluconate disinfection for cesarean section of pregnant obese pregnant women can reduce the occurrence of incision fat liquefaction and infection, so as to achieve the purpose of promote rehabilitation and reduce hospitalization expenses.